If you purchased a 3 user for Backup Buddy and want to upgrade to the 10, is there a migration path, or do you just end up with 13? And if you install BUB on a site, then take the site down, what is the procedure to migrate the license to another site? Just De-Activate then reinstall?

What "3 user" license are you referring to? There is the personal license for 2 sites.

And the way we do upgrades, is you just pay for the price difference between the 2 and the 10. So you are only paying for, and receiving, 10 licenses.

To move the plugin license from a site, yes, just "un-license" it from a site. There is actually a button that says "Unlink license from site" and that would do the trick. If you leave the plugin licensed on the site, it will count as one of the ten.